abDrugOverlapAnalysis: abDrugOverlapAnalysis

In biodev/packageDir: Tool for in silico functional analysis design and exploration of relation between genomic function and aberration.

Description

main function for running analysis of functional and genomic aberration arms

Usage

abDrugOverlapAnalysis(study, thresh = 0.05,
  enrich_col = "hyperg_p_w_FDR", verbose = T, settings = NULL)

Arguments

study	A study object (must have results loaded for aberration and functional analyses)
thresh	Numeric, the threshold used to establish which pathways will be considered to be drug sensitive and aberrational.
enrich_col	String, the name of the column in the path summary used to determine significance of a pathway. This is the column to which the threshold argument is to be applied.
verbose	Logical, a flag indicating if the program is to provide extra diagnostic output.
settings	List obejct. This contains the settings used in the overlap analysis. Use getDefaultOverlapSettings()

Value

Study object with overlap analysis in results list added or replaced

Examples

#get a study object pre-loaded with genomic aberration and functional genomic data.
stud = getTestStudyObject()

#get default overlap analysis settings
defSettings = getTestStudySettings()
overlapSettings = defSettings$overlap_analysis

#run the overlap analysis

overlapRes1 = abDrugOverlapAnalysis(study=stud, settings=overlapSettings)

## Not run: 
#If settings for the overlap analysis cannot be found, the overlap 
#analysis will run in interactive mode, requiring user input.
#This line of code will run the overlap anaysis in interactive mode, 
#requesting user input to establish settings:

abDrugOverlapAnalysis(study=stud)

## End(Not run)

biodev/packageDir documentation built on Nov. 4, 2019, 7:19 a.m.